syang11 / KNN

Inferring RNA sequence preferences for poorly studied RNA-binding proteins based on co-evolution

Welcome!

This repo stores codes and data for the paper:

Shu Yang, Junwen Wang, Raymond Ng. Inferring RNA sequence preferences for poorly studied RNA-binding proteins based on co-evolution. BMC Bioinformatics. 2018.

It contains:

1. Scripts and instructions for the KNN method presented in the paper. And supplementary data for performance results.
2. An extended implementation of the RCK program, called KNN-RCK which takes an input PWM as its sequence model.
3. Predicted sequence preference in the form of PWM for ~1000 poorly studied proteins which have no binding preference information available before.